Comparative population genomics of latitudinal variation in <i>Drosophila simulans</i> and <i>Drosophila melanogaster</i>

Machado, Heather E.; Bergland, Alan O.; O’Brien, Katherine R.; Behrman, Emily L.; Schmidt, Paul S.; Petrov, Dmitri A.

doi:10.1111/mec.13446

Cited by 132 publications

(174 citation statements)

References 105 publications

(218 reference statements)

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“…This is further supported by the observation that there is significant overlap in differentiated genes between D. simulans and D. melanogaster (Machado et al 2015;Zhao et al 2015). This between-species parallel differentiation in both gene expression and allele frequency (Machado et al 2015) raises the additional possibility that weaker phenotypic clines generally reported for D. simulans may not accurately reflect the influence of spatially varying selection on this species.To further investigate patterns of geographic differentiation in D. simulans and similarities and differences with respect to D. melanogaster, we resequenced four D. simulans populations-one northern and one southern-in both North America and Australia. We then employed an F ST outlier approach to identify putative targets of spatially varying selection.…”

supporting

confidence: 65%

supporting

confidence: 65%

“…For example, D. melanogaster appears to be more tolerant of high ethanol concentrations, and the two species differ in their seasonal abundances and thermal tolerances (Parsons 1975b(Parsons , 1977. Moreover, it is known that their geographic centers of diversity vary, with D. melanogaster being most diverse in South-Central Africa While differences in the strength of clinal variation in D. simulans compared to D. melanogaster may suggest that the two species are responding to their local environments in different ways, the findings of Machado et al (2015), differentiation in patterns of gene expression , and phenotypic clines in traits such as body size indicate that D. simulans is likely evolving, in at least some capacity, to spatially varying selection. This is further supported by the observation that there is significant overlap in differentiated genes between D. simulans and D. melanogaster (Machado et al 2015;Zhao et al 2015).…”

mentioning

confidence: 70%

“…Moreover, it is known that their geographic centers of diversity vary, with D. melanogaster being most diverse in South-Central Africa While differences in the strength of clinal variation in D. simulans compared to D. melanogaster may suggest that the two species are responding to their local environments in different ways, the findings of Machado et al (2015), differentiation in patterns of gene expression , and phenotypic clines in traits such as body size indicate that D. simulans is likely evolving, in at least some capacity, to spatially varying selection. This is further supported by the observation that there is significant overlap in differentiated genes between D. simulans and D. melanogaster (Machado et al 2015;Zhao et al 2015). This between-species parallel differentiation in both gene expression and allele frequency (Machado et al 2015) raises the additional possibility that weaker phenotypic clines generally reported for D. simulans may not accurately reflect the influence of spatially varying selection on this species.…”

mentioning

confidence: 80%

“…One potential interpretation of this is a relative lack of local adaptation in D. simulans. More recently, Machado et al (2015) found genomic evidence for clinal variation in D. simulans and verified that it is less pronounced than in D. melanogaster.…”

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confidence: 99%

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Genomic Patterns of Geographic Differentiation in Drosophila simulans

2016

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Geographic patterns of genetic differentiation have long been used to understand population history and to learn about the biological mechanisms of adaptation. Here we present an examination of genomic patterns of differentiation between northern and southern populations of Australian and North American Drosophila simulans, with an emphasis on characterizing signals of parallel differentiation. We report on the genomic scale of differentiation and functional enrichment of outlier SNPs. While, overall, signals of shared differentiation are modest, we find the strongest support for parallel differentiation in genomic regions that are associated with regulation. Comparisons to Drosophila melanogaster yield potential candidate genes involved in local adaptation in both species, providing insight into common selective pressures and responses. In contrast to D. melanogaster, in D. simulans we observe patterns of variation that are inconsistent with a model of temperate adaptation out of a tropical ancestral range, highlighting potential differences in demographic and colonization histories of this cosmopolitan species pair.KEYWORDS geographic variation; population genomics; Drosophila T HE geographic distribution of genetic or phenotypic variation can provide valuable insight into the process of adaptation. For example, consistent patterns of genetic variation across space have long been interpreted as evidence for local adaptation owing to spatially varying selection (Endler 1977; Adrion et al. 2015). This is well illustrated in populations of Drosophila melanogaster, a model system showing consistent phenotypic and molecular clines across environmental gradients (Hoffmann and Weeks 2007). Among these, the association of latitude with variation in ecologically relevant traits such as heat knockdown resistance, chill coma recovery, and diapause incidence Schmidt and Paaby 2008) provides strong support for local adaptation to climate.Despite efforts to understand the potential adaptive nature of molecular variation in populations of Drosophila, there remains some disconnect between our understanding of allele-frequency clines and phenotypic clines, of which the latter are more easily and intuitively interpretable. For the vast majority of clinal molecular polymorphisms in Drosophila, the mechanisms underlying their maintenance are poorly understood. Nevertheless, because gene flow in Drosophila is thought to be high, strong differentiation often can be argued as evidence of local adaptation. Moreover, because the physical scale of linkage disequilibrium (LD) in Drosophlia is often smaller than the size of genes (Langley et al. 2012), differentiation between populations generally is associated with hypotheses regarding individual genes as targets of selection.Observation of parallel patterns of differentiation furthers the argument for an adaptive basis to differentiation, and in general, comparisons of patterns of variation across independent replicate geographic transects may contribute to an understanding of...

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confidence: 65%

supporting

confidence: 65%

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confidence: 70%

mentioning

confidence: 80%

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confidence: 99%

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Genomic Patterns of Geographic Differentiation in Drosophila simulans

2016

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Experimental evolution supports signatures of sexual selection in genomic divergence

et al. 2021

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Comparative genomics has contributed to the growing evidence that sexual selection is an important component of evolutionary divergence and speciation. Divergence by sexual selection is implicated in faster rates of divergence of the X chromosome and of genes thought to underlie sexually selected traits, including genes that are sex biased in expression. However, accurately inferring the relative importance of complex and interacting forms of natural selection, demography, and neutral processes that occurred in the evolutionary past is challenging. Experimental evolution provides an opportunity to apply controlled treatments for multiple generations and examine the consequent genomic divergence. Here, we altered sexual selection intensity, elevating sexual selection in polyandrous lines and eliminating it in monogamous lines, and examined patterns of allele frequency divergence in the genome of Drosophila pseudoobscura after more than 160 generations of experimental evolution. Divergence is not uniform across the genome but concentrated in “islands,” many of which contain candidate genes implicated in mating behaviors and other sexually selected phenotypes. These are more often seen on the X chromosome, which also shows greater divergence in FST than neutral expectations. There are characteristic signatures of selection seen in these regions, with lower diversity on the X chromosome than the autosomes, and differences in diversity on the autosomes between selection regimes. Reduced Tajima's D within some of the divergent regions may imply that selective sweeps have occurred, despite considerable recombination. These changes are associated with both differential gene expression between the lines and sex‐biased gene expression within the lines. Our results are very similar to those thought to implicate sexual selection in divergence between species and natural populations, and hence provide experimental support for the likely role of sexual selection in driving such types of genetic divergence, but also illustrate how variable outcomes can be for different genomic regions.

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Population Genomics on the Fly: Recent Advances in Drosophila

Haudry

Laurent

Kapun

2020

Methods in Molecular Biology

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Drosophila melanogaster, a small dipteran of African origin, represents one of the best-studied model organisms. Early work in this system has uniquely shed light on the basic principles of genetics and resulted in a versatile collection of genetic tools that allow to uncover mechanistic links between genotype and phenotype. Moreover, given its world-wide distribution in diverse habitats and its moderate genome-size, Drosophila has proven very powerful for population genetics inference and was one of the first eukaryotes whose genome was fully sequenced. In this bookchapter, we provide a brief historical overview of research in Drosophila and then focus on recent advances during the genomic era. After describing different types and sources of genomic data, we discuss mechanisms of neutral evolution including the demographic history of Drosophila and the effects of recombination and biased gene conversion. Then, we review recent advances in detecting genome-wide signals of selection, such as soft and hard selective sweeps. We further provide a brief introduction to background selection, selection of non-coding DNA and codon usage and focus on the role of structural variants, such as transposable elements and chromosomal inversions, during the adaptive process. Finally, we discuss how genomic data helps to dissect neutral and adaptive evolutionary mechanisms that shape genetic and phenotypic variation in natural populations along environmental gradients. In summary, this book chapter serves as a starting point to Drosophila population genomics and provides an introduction to the system and an overview to data sources, important population genetic concepts and recent advances in the field.

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Comparative population genomics of latitudinal variation in Drosophila simulans and Drosophila melanogaster

Cited by 132 publications

References 105 publications

Genomic Patterns of Geographic Differentiation in Drosophila simulans

Genomic Patterns of Geographic Differentiation in Drosophila simulans

Experimental evolution supports signatures of sexual selection in genomic divergence

Population Genomics on the Fly: Recent Advances in Drosophila

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